as_subfeats: Compute a layout for subfeat data

In gggenomes: A Grammar of Graphics for Comparative Genomics

Compute a layout for subfeat data

Description

Read subfeat data such as domains or blast hits on genes into a tidy dataframe. Subfeats need to be associated with an already added feat track. The subfeat track itself is internally converted into a new, regular feat track by mapping the start and end coordinates provided relative to their parent feat into coordinates relative to the sequences underlying the parent feats.

Usage

as_subfeats(x, seqs, feats, ..., everything = TRUE)

## S3 method for class 'tbl_df'
as_subfeats(
  x,
  seqs,
  feats,
  ...,
  everything = TRUE,
  transform = c("none", "aa2nuc", "nuc2aa")
)

Arguments

x	subfeat data convertible to a feat layout
seqs	the sequence layout the parent feats map onto.
feats	the parent feats the subfeats map onto.
...	passed on to layout_seqs() spaces, i.e. if matching nucleotide-level annotations to protein level annotations, e.g. genes and protein blast results.
everything	set to FALSE to drop optional columns
transform	use if feats and subfeats are in different coordinate

Details

Obligatory columns are feat_id, start and end. Also recognized are strand and bin_id.

Note start and end for every record will be coerced so that start < end. If no strand was provided, strand will be added and set to "+" for records that initially had start < end and "-" for end < start inputs. If strand was provided, start and end will be reorganized to conform with start < end without any additional effect.

Value

a tbl_df with plot coordinates

Methods (by class)

• as_subfeats(tbl_df): Convert a list of tibbles into a feat layout

gggenomes documentation built on Sept. 11, 2024, 8:55 p.m.